--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/ProteinProtonator.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,39 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Preparation]-->
+<tool id="ProteinProtonator" name="ProteinProtonator" version="1.1.0">
+  <description>protonate protein structures</description>
+  <macros>
+    <token name="@EXECUTABLE@">ProteinProtonator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ProteinProtonator
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_ph:
+  -ph $param_ph
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
+    <param name="param_ph" type="float" value="7.0" label="pH-value for pH-dep. protonation" help="(-ph) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="pdb"/>
+  </outputs>
+  <help>ProteinProtonator allows you add hydrogens to a protein structure.
+
+Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
+
+Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.
+
+</help>
+</tool>